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I'm not sure the ToC glitch arises as a direct result of bulk conversions (?).
When the ToC for a single ePub (new or converted) is being created (or regenerated to make corrections) using various "edit TOC" functions, there will be a problem if the ePub has multiple parts and each part re-starts the numbering for the chapters.
As an example, if a book has five parts, and the parts have from three to eight numbered chapters each, then the total number of chapters in the ToC will be eight because all the other chapters will be considered to be "duplicative"
Multi-part Omnibus editions would be a problem only where the chapter headers are non-descriptive (e.g. Chapter 1), and therefore would appear duplicative from one part to the next.
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